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I guess you could use calibre's EPUBMerge/Split plugins... but they put each book in a separate folder of the resulting EPUB. Sigil automatically flattens that and restructures the file tree, which can sometimes badly mess up such a book. IIRC there were filename collisions.
Probably what happened to your omnibus.
calibre's editor is immune to that, because it does not enforce structure automatically.
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